[gmx-users] REMD

Dongsheng Zhang dong at pampas.chem.purdue.edu
Thu Apr 13 08:42:20 CEST 2006

dear Mark,

Thank you very much for your prompt reply.  I try to use parallel
computing. It works fine.
for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle     
             to  get replica0.tpr
             then, mdrun_mpi -np 2 -s replica0.tpr

The error message mentioned in the previous email looks very strange to
me. MPI works fine, and individual tpr runs fine. The error message
comes out before replica exchange. replica0 stops at step 500, replica1
stops at step 400, even the output informatio can't be complted. The
last lines in replica1.log is

        Step           Time         Lambda
            400        0.80000        0.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS

I hope these further information can help you to figure out what's the

Best Wishes!


On Thu, 2006-04-13 at 15:17 +1000, Mark Abraham wrote: 
> > Dear gmx users:
> >
> > I am trying to run REMD with two replicas (for testing). I used
> > grompp -f -c -p -o replica0 to get replica0.tpr
> > grompp -f -c -p -o replica1 to get replica1.tpr
> >
> > then used
> > mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica
> > -v -N 2
> > to run it.
> mdrun doesn't take '-N 2' but I'm not sure this is the problem. Otherwise,
> looks fine to me.
> > I got an error message "Segmentation fault" from my script output, but
> > no error message in both log files. When I tried to run individual tpr
> > file, it worked fine.
> >
> > Could someone can comment why I got "Segmentation fault"? Thank you for
> > your help!
> Your MPI setup might require you use a command like "mpirun -N 2 mdrun_mpi
> ..." to make it work - the segfault might be a gromacs-MPI interaction
> problem. If you can run an MPI process from the command line you may get
> more helpful feedback.
> Mark
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